Global systems-level analysis of Hfq and SmpB deletion mutants in Salmonella: implications for virulence and global protein translation.
Charles Ansong,Hyunjin Yoon,Steffen Porwollik,Heather M. Mottaz-Brewer,Brianne O. Petritis,Navdeep Jaitly,Joshua N. Adkins,Michael McClelland,Fred Heffron,Richard D. Smith +9 more
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TLDR
It is shown that mutants of hfq and smpB directly or indirectly modulate at least 20% and 4% of all possible Salmonella proteins, respectively, with limited correlation between transcription and protein expression.Abstract:
Using sample-matched transcriptomics and proteomics measurements it is now possible to begin to understand the impact of post-transcriptional regulatory programs in Enterobacteria. In bacteria post-transcriptional regulation is mediated by relatively few identified RNA-binding protein factors including CsrA, Hfq and SmpB. A mutation in any one of these three genes, csrA, hfq, and smpB, in Salmonella is attenuated for mouse virulence and unable to survive in macrophages. CsrA has a clearly defined specificity based on binding to a specific mRNA sequence to inhibit translation. However, the proteins regulated by Hfq and SmpB are not as clearly defined. Previous work identified proteins regulated by hfq using purification of the RNA-protein complex with direct sequencing of the bound RNAs and found binding to a surprisingly large number of transcripts. In this report we have used global proteomics to directly identify proteins regulated by Hfq or SmpB by comparing protein abundance in the parent and isogenic hfq or smpB mutant. From these same samples we also prepared RNA for microarray analysis to determine if alteration of protein expression was mediated post-transcriptionally. Samples were analyzed from bacteria grown under four different conditions; two laboratory conditions and two that are thought to mimic the intracellular environment. We show that mutants of hfq and smpB directly or indirectly modulate at least 20% and 4% of all possible Salmonella proteins, respectively, with limited correlation between transcription and protein expression. These proteins represent a broad spectrum of Salmonella proteins required for many biological processes including host cell invasion, motility, central metabolism, LPS biosynthesis, two-component regulatory systems, and fatty acid metabolism. Our results represent one of the first global analyses of post-transcriptional regulons in any organism and suggest that regulation at the translational level is widespread and plays an important role in virulence regulation and environmental adaptation for Salmonella.read more
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Omic data from evolved E. coli are consistent with computed optimal growth from genome‐scale models
Nathan E. Lewis,Kim K. Hixson,Tom M Conrad,Joshua A. Lerman,Pep Charusanti,Ashoka D. Polpitiya,Joshua N. Adkins,Gunnar Schramm,Gunnar Schramm,Samuel O. Purvine,Daniel Lopez-Ferrer,Karl K. Weitz,Roland Eils,Roland Eils,Rainer König,Rainer König,Richard D. Smith,Bernhard O. Palsson +17 more
TL;DR: In this article, the authors reported that >98% of active reactions from FBA optimal growth solutions are supported by transcriptomic and proteomic data, and when E. coli adapts to growth rate selective pressure, the evolved strains upregulated genes within the optimal growth predictions, and downregulated genes outside of the optimal solutions.
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Global RNA recognition patterns of post-transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo.
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